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LOC123575661 Sharpr-MPRA regulatory region 15549 [ Homo sapiens (human) ]

Gene ID: 123575661, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575661
Gene description
Sharpr-MPRA regulatory region 15549
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Dec 2021]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (5208755..5209049)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (5077963..5078257)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (5208989..5209283)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene LYRM4 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:5085857-5086546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23901 Neighboring gene LYR motif containing 4 Neighboring gene MPRA-validated peak5632 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5130070-5130656 Neighboring gene protein phosphatase 1 regulatory subunit 3G Neighboring gene Sharpr-MPRA regulatory region 2533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5193017-5193524 Neighboring gene microRNA 3691 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:5230418-5231617 Neighboring gene uncharacterized LOC124901249 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23902 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23903 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23904 Neighboring gene Sharpr-MPRA regulatory region 4425 Neighboring gene phenylalanyl-tRNA synthetase 2, mitochondrial Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:5368745-5369944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23906 Neighboring gene NANOG hESC enhancer GRCh37_chr6:5412113-5412622 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:5438556-5439472 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:5439473-5440389 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5456946-5457932 Neighboring gene FARS2 antisense RNA 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_077920.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    5208755..5209049
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    5077963..5078257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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